Single-molecule conductance of functionalized oligoynes: Length dependence and junction evolution

Article abstract of DOI:10.1021/ja4015293

We report a combined experimental and theoretical investigation of the length dependence and anchor group dependence of the electrical conductance of a series of oligoyne molecular wires in single-molecule junctions with gold contacts. Experimentally, we focus on the synthesis and properties of diaryloligoynes with n = 1, 2, and 4 triple bonds and the anchor dihydrobenzo[b]thiophene (BT). For comparison, we also explored the aurophilic anchor group cyano (CN), amino (NH₂), thiol (SH), and 4-pyridyl (PY). Scanning tunneling microscopy break junction (STM-BJ) and mechanically controllable break junction (MCBJ) techniques are employed to investigate single-molecule conductance characteristics. The BT moiety is superior as compared to traditional anchoring groups investigated so far. BT-terminated oligoynes display a 100% probability of junction formation and possess conductance values which are the highest of the oligoynes studied and, moreover, are higher than other conjugated molecular wires of similar length. Density functional theory (DFT)-based calculations are reported for oligoynes with n = 1-4 triple bonds. Complete conductance traces and conductance distributions are computed for each family of molecules. The sliding of the anchor groups leads to oscillations in both the electrical conductance and the binding energies of the studied molecular wires. In agreement with experimental results, BT-terminated oligoynes are predicted to have a high electrical conductance. The experimental attenuation constants β_H range between 1.7 nm^-1 (CN) and 3.2 nm^-1 (SH) and show the following trend: β _H(CN) < β_H(NH₂) < β_H(BT) < β_H(PY) ≈ β_H(SH). DFT-based calculations yield lower values, which range between 0.4 nm ^-1 (CN) and 2.2 nm^-1 (PY).

Full text of DOI:10.1021/ja4015293

Article
pubs.acs.org/JACS
Single-Molecule Conductance of Functionalized Oligoynes: Length
Dependence and Junction Evolution
Pavel Moreno-García,†,∥,⊥ Murat Gulcur,‡,⊥ David Zsolt Manrique,§,⊥ Thomas Pope,§,⊥ Wenjing Hong,†
Veerabhadrarao Kaliginedi,† Cancan Huang,† Andrei S. Batsanov,‡ Martin R. Bryce,*,‡ Colin Lambert,*,§
and Thomas Wandlowski*,†
†Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
‡Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
§Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
∥Instituto de Física, Benemer
ita Universidad Autonoma de Puebla, Apartado Postal J-48, Puebla 72570, Mexico
́ ́ ́
S
* Supporting Information
ABSTRACT: We report a combined experimental and theoretical investigation of the length dependence and anchor group
dependence of the electrical conductance of a series of oligoyne molecular wires in single-molecule junctions with gold contacts.
Experimentally, we focus on the synthesis and properties of diaryloligoynes with n = 1, 2, and 4 triple bonds and the anchor
dihydrobenzo[b]thiophene (BT). For comparison, we also explored the aurophilic anchor group cyano (CN), amino (NH2),
thiol (SH), and 4-pyridyl (PY). Scanning tunneling microscopy break junction (STM-BJ) and mechanically controllable break
junction (MCBJ) techniques are employed to investigate single-molecule conductance characteristics. The BT moiety is superior
as compared to traditional anchoring groups investigated so far. BT-terminated oligoynes display a 100% probability of junction
formation and possess conductance values which are the highest of the oligoynes studied and, moreover, are higher than other
conjugated molecular wires of similar length. Density functional theory (DFT)-based calculations are reported for oligoynes with
n = 1−4 triple bonds. Complete conductance traces and conductance distributions are computed for each family of molecules.
The sliding of the anchor groups leads to oscillations in both the electrical conductance and the binding energies of the studied
molecular wires. In agreement with experimental results, BT-terminated oligoynes are predicted to have a high electrical
conductance. The experimental attenuation constants βH range between 1.7 nm−1 (CN) and 3.2 nm−1 (SH) and show the
following trend: βH(CN) < βH(NH2) < βH(BT) < βH(PY) ≈ βH(SH). DFT-based calculations yield lower values, which range
between 0.4 nm−1 (CN) and 2.2 nm−1 (PY).
rings or by bond rotations.15 Theoretical studies have predicted
INTRODUCTION
■
that polyynes should have excellent intramolecular electron-
and charge-transport properties, exhibiting efficient molecular
wire behavior.16−18 In this regard, experimental studies are very
much an open issue.
Polyynes possess reduced stability with increasing length of
the sp chain. The main strategies to stabilize longer derivatives
are to terminate the chains with bulky aryl or organometallic
groups18−21 or to shield the polyyne backbone.22,23 Without
Conjugated polyyne molecules are of interest as a family of
carbon-rich backbones.1−3 They comprise an array of sp-
hybridized carbon atoms with alternating single and triple
bonds and almost cylindrical electron delocalization in a one-
dimensional chain.2,4,5 Polyynes and shorter sp oligomers
(oligoynes) have been proposed for molecular electronics
applications (wires, switches, nonlinear optics, etc.).6,7 Their
study is therefore of both fundamental and economic interest.
Unlike oligo(phenylenevinylene) (OPV)8−10 and oligo-
(phenyleneethynylene) (OPE),11−14 the conjugation over the
oligo/polyyne carbon backbone is not interrupted by phenyl
Received: February 11, 2013
© XXXX American Chemical Society
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a
Scheme 1. Structures of the Molecules Discussed in This Work and Their Nomenclature
a
SH1, SH2, and SH4 were isolated as the bis(thioacetate) derivatives.
such stabilizing groups, polyynes which are longer than eight
acetylenic carbons (i.e., tetrayne derivatives) tend to decom-
pose or polymerize rapidly at room temperature.24,25 By using
very bulky tris(3,5-di-t-butylphenyl)methyl end groups, poly-
ynes comprising up to 44 contiguous carbons have been
characterized under normal laboratory conditions.26 Optical
spectroscopic studies in solution showed that these systems
exist as alternating single and triple bonds with a very low
HOMO−LUMO gap.
A standard protocol for accurately assessing the charge
transport through single or a few molecules is to anchor the
molecule(s) between metal electrodes (often gold) and to
study the electronic properties of the metal−molecule−metal
junction by scanning tunneling microscopy (STM) or
mechanically controllable break junction (MCBJ) meth-
ods.25−31 This requires molecules to be terminated by
functional groups, which have relatively high binding strengths
to gold, e.g. thiol,32,33 pyridyl,34−36 and amino.37 However,
functional groups at the terminal positions can react (inter- or
intramolecularly) with the sp backbone to form polymer-like
structures,38 and the bulky terminal groups, which are known to
stabilize longer polyynes, are not suitable for anchoring the
molecules to metal surfaces. Therefore, it remains a
considerable challenge to synthesize oligoynes or polyynes
with end-groups which will anchor the molecule to gold (as
well as to other conducting leads) and will be stable to
purification and handling under ambient conditions. Funda-
mentally new aspects of synthetic oligoyne chemistry need to
be developed to enable these π-systems to be exploited in
molecular junctions. In this context, the first examples were
stable 4-pyridyl (PY) end-capped derivatives up to a C8
(tetrayne) chain length (PY(−CC)n−PY; n = 1, 2, 4).
Their electrical properties were studied in STM-BJ experi-
ments.39 Subsequently a molecule with a C8 chain between two
bulky triarylphosphine-Pt(II) centers bearing thiol end groups
was studied in MCBJ experiments.40 Two very recent papers
reported single-molecule charge-transport characteristics of
short-chain (n = 1) tolane derivatives.36,41 However, these
reports do not address the challenge of the synthesis,
characterization, and electrical measurement of longer analogs
which is the focus of the present article. We now describe, for
the first time, a comprehensive family of diaryloligoyne
molecular wires Ar(−CC)n−Ar, n = 1, 2, 4, with five
different terminal functionalities (Scheme 1).
We focus on the diaryloligoynes (n = 2, 4) under ambient
laboratory conditions. Comparisons are made with the
corresponding diarylacetylene (tolane) derivatives (n = 1).
We explore charge transport characteristics and address the
effect of the molecular length on the conductance of these
a
Scheme 2. Synthesis of BT1, BT2, and BT4
a
(i) TMSA, [Pd(PPh3)4], CuI, (i-Pr)2NH, THF, rt, 4 h, 95%; (ii) TBAF, THF, rt, 15 min, 92%; (iii) 2a, [Pd(PPh3)4], CuI, (i-Pr)2NH, THF, rt, 4 h,
75%; (iv) Cu(OAc)2·H2O, pyridine, MeOH, rt, 12 h, 86%; (v) HCC−CC−TMS, [Pd(PPh3)4], (i-Pr)2NH, THF, rt, 4 h, 78%; (vi) Cu(OAc)2·
H2O, pyridine, MeOH, rt, 12 h, 77%.
B
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Article
experiment. The STM tips were uncoated, electrochemically etched
gold wires (Goodfellow, 99.999%, 0.25 mm diameter). The solutions
were prepared from 1,3,5-trimethylbenzene (TMB, Aldrich, p.a.) and
tetrahydrofuran (THF, Aldrich, p.a.), volume ratio 4:1, containing 0.1
mM of the target molecules. The substrate surface was inspected by
STM imaging before the start of each set of iT−Δz measurements.
Typically, we recorded up to 10 000 individual traces with a pulling
rate of 58 nm s−1.
The MCBJ experiments are based on the trapping of individual
molecules between two atomically sharp gold wires (99.999%,
Goodfellow, 100 μm diameter), freely suspended and supported on
a sheet of spring steel. The latter is bent by a pushing rod, whose
vertical movement is controlled by a stepper motor in combination
with a piezo stack. The usual moving rate of the pushing rod was 3 to
150 nm s−1, which translates into an opening respective closing rate of
0.1−5 nm s−1. Typically, we recorded up to 2000 stretching cycles to
obtain statistically significant data.
The high mechanical stability of the MCBJ setup allowed also the
simultaneous acquisition of current−bias voltage characteristics (iT−
Vbias) during the stretching process. We reduced the piezo rate in these
experiments to 10 nm s−1 and swept Vbias continuously between −1.00
and +1.00 V with 40 V s−1. We recorded 500 data points per iT−Vbias
curve and acquired ca. 25 traces per second. Typically, we measured
20−50 individual curves during the various stages of one single
breaking cycle. Further technical details of our MCBJ setup as well as
of our measuring routines are described in refs 36 and 42. Finally, we
note that the solutions were the same as in the complementary STM
measurements.
Theoretical Methods. Electronic and transport calculations of the
five oligoyne series with BT, SH, PY, NH2, CN anchor groups were
performed with the ab initio code SMEAGOL,52,53 which uses the
Hamiltonian provided by the DFT code SIESTA54 in combination
with the nonequilibrium Green’s function formalism. SIESTA employs
nonconserving pseudopotentials to account for the core electrons and
a linear combination of pseudoatomic orbitals. SMEAGOL divides the
entire nanoscale junction into three parts: the left and the right bulk
electrodes simulated by multiple gold layers grown along the (111)
direction and the “extended molecule” that consists of the molecule
and gold pyramids modeling the tip and the electrode. SMEAGOL
uses the Hamiltonian derived from SIESTA to calculate self-
consistently the density matrix, the transmission coefficients T(E) of
the electrons from the left to the right lead, and the iT−Vbias
characteristics. Further details about the above computation methods,
the energy level alignment, and simulations of the conductance versus
distance traces are given in the SI.
families of oligoynes by performing single-molecule transport
measurements for the stable derivatives using complementary
STM-BJ34,36 and MCBJ8,42 techniques. DFT-based calculations
provide additional insights into the electronic structure of our
molecular junctions. The paper will particularly demonstrate
the superior structure and electronic properties of the
dihydrobenzo[b]thiophene (BT) anchoring group attached to
a carbon-rich backbone for charge transport studies in (single)
molecular junctions.
EXPERIMENTAL SECTION
■
Synthesis of Diaryloligoynes. Diarylacetylene (tolane) com-
pounds Ar1 were synthesized by Sonogashira couplings between the
corresponding arylacetylene and aryl iodide derivatives.43 Compounds
PY2, NH22, and CN2 derivatives were synthesized by oxidative
dimerization of arylacetylenes.44,45 The diarylbutadiyne derivatives
SH2 [as the bis(thioacetate) derivative], BT2, and all diaryltetrayne
derivatives Ar4 were synthesized by dimerization of trimethylsilyl-
protected precursor compounds under Eglington−Galbraith coupling
conditions [Cu(OAc)2·H2O, pyridine, methanol] (Scheme SI-1).44−47
We have also synthesized the BT end-capped compounds BT1, BT2,
and BT4, which to our knowledge is the first series of molecules to
incorporate this anchor group. The use of this anchor group was
motivated by a recent report on the transport properties of compound
1 in metal−molecule−metal junctions.48
During the preparation of this manuscript Szafert et al. reported the
synthesis of CN4 using similar methodology.49
The reported synthetic route to 1 (by reduction of the parent
benzo[1,2-b:4,5-b′]dithiophene) is not applicable to the functionalized
derivatives required for the BT series in the present work, so a new
synthetic strategy for functionalization of BT was required. The
syntheses of compounds BT1, BT2, and BT4 starting from the novel
iodo derivative 2a are shown in Scheme 2.
The diyne derivatives Ar2 are all stable to storage in air at room
temperature. An initial aspect of the work was to establish how the
stability of the tetrayne derivatives Ar4 is dependent on the
functionality on the head groups, as this will determine which
derivatives are suitable for molecular junction formation. Earlier work
showed that primary amines readily react with oligoyne chains38 and
that 2-aminophenyl end-capped tetrayne reacts intramolecularly to
form indole derivatives in the presence of a copper salt.47 We have
found that compounds PY4, CN4, and BT4 are all very stable under
ambient conditions. NH24 is light sensitive and less stable, which
precluded the use of this molecule in junction formation in the present
study. Compound SH4 [bis(thioacetate) derivative] decomposed
rapidly, and it could not be purified. However, a UV−vis absorption
spectrum of the reaction mixture (Figure S4) showed a significant red
shift compared to SH2, and the vibronic features are consistent with
the formation of the tetrayne SH4. The X-ray crystal structures of
CN4, BT4, and BT2 are discussed in the Supporting Information (SI).
Conductance Distance Measurements. The transport proper-
ties of single molecular wires were studied using STM-BJ33,34 and
complementary MCBJ8,42 measurements in solution, at room
temperature, and under argon. The STM-BJ approach is based on
the repeated formation and breaking of a vertical (single) molecule
junction between an atomically sharp gold STM tip and a flat Au(111)
RESULTS AND DISCUSSION
■
Dihydrobenzo[b]thienyl-capped oligoyne series (BT):
Conductance Measurements. STM-BJ and MCBJ Con-
ductance Measurements. Figure 1A displays three typical
sample sets of conductance (G) versus distance (Δz) stretching
traces, plotted in a semilogarithmic scale, as recorded for the
three BT-capped oligoynes BT1, BT2, and BT4 in TMB/THF
using the STM-BJ approach. After formation of the contact
between the gold tip and the Au(111) substrate, the tip was
withdrawn with a rate of 58 nm s−1. All curves show initially a
step-like decrease of the conductance from 10 G0 up to 1 G0;
G0 = 2e2/h = 77.5 μS being the quantum of conductance.
Subsequently, the conductance decreases by several orders in
magnitude, which is assigned to the “jump out of contact”.55
The gold contacts retract suddenly by (0.5 0.1) nm, the so-
called snap-back distance Δzcorr (see SI and refs 36, 55, and 56
for details). Additional features, such as single and multi
conductance plateaus, are observed at G ≤ G0, which are
attributed to the formation of (single) molecular junctions. The
noise level is reached at G < 10−6 G0 in the STM-BJ
experiments.
substrate, and the simultaneous monitoring of the current iT or
34
conductance G = iT/Vbias at constant bias voltage Vbias
.
The MCBJ
technique relies on the formation and rupture of molecular junctions
between horizontally suspended gold wires.42
The STM-BJ experiments were carried out with a modified
Molecular Imaging Pico SPM equipped with a dual-channel
preamplifier and housed in an all-glass argon-filled chamber.13,50 The
current (iT)−distance (Δz) measurements were performed with a
separate, lab-built analog ramp unit. For further technical details we
refer to our previous work.13,51 The sample electrodes were Au(111)
disks, 2 mm height, and 10 mm in diameter or gold single-crystal bead
electrodes. The Au(111) substrates were flame annealed before each
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Figure 2. (A) Characteristic displacement histograms from STM-BJ
experiments as analyzed for BT1, BT2, and BT4 in the high
conductance region. (B) Comparison of characteristic displacement
histograms of BT1 obtained from the high (H: 0.7 G0−3.2 × 10−4 G0)
and in the low (L: 0.7 G0−10−6 G0) conductance regions of the 2D
conductance versus displacement histograms (Figure 1 and SI).
In addition, BT1 and BT2 revealed a second, rather broad
and lower conductance feature GL with maxima at (0.8 0.2)·
10−5 G0 and (0.30 0.03)·10−5 G0 for BT concentrations larger
than 0.01 mM (Figure S18), respectively. The STM-BJ
experiments did not resolve a low conductance GL for the
longest oligoyne BT4, most probably due to superposition with
the noise level.
The above analysis was extended by constructing 2D
conductance versus displacement histograms.51,57 This repre-
sentation provides direct access to the evolution of molecular
junctions during the formation, stretching, and breakdown
steps. Figure 1C displays, as a typical example, the data for
BT1. (The corresponding plots of BT2 and BT4 are shown in
SI.) The individual G−Δz traces were aligned by setting the
common origin to 0.7 G0. The data of Figure 1C reveal
quantized conductance features at G ≥ 1 G0. They correspond
to the breaking of gold−gold contacts. Additional high-density
data clouds are observed in 3.3 × 10−4 G0 ≤ GH ≤ 10−2 G0 and
10−6 G0 ≤ GL ≤ 3.2 × 10−5 G0, centered on 3.2 × 10−3 G0 and
10−5 G0, respectively. These regions represent the high- and the
low-conductance states of derivative BT1. The 2D histogram in
Figure 1C demonstrates further that both the high and the low
conductances decrease monotonously with increasing relative
displacement (or junction elongation) Δz.
The results of the STM-BJ experiments are supported by
corresponding MCBJ measurements (cf. Figure 1D−F and SI).
Table 1 compiles the most probable conductance values of GH*
and GL* of the three BT derivatives. The conductances GH are
significantly higher than reported values of other conjugated
molecular wires of similar length.10,13,58−60 We also note that
the higher sensitivity of our MCBJ setup allowed an estimate of
the most probable low conductance of BT4, which was
obtained as GL* ≈ 0.1 × 10−5 G0.
Stretching Distance and Junction Formation Probability.
Analyzing the evolution of a molecular junction upon stretching
provides additional information about stability and transitions
between the two conductance states H and L. We constructed
relative displacement (Δz) histograms36 by calculating the
displacement from the relative zero position at 0.7 G0 (Gmax as
upper limit) to the end of the high (low) conductance region of
every individual trace. The lower limit Gmin is defined as 1 order
of magnitude beneath the most probable high (low)
conductances GH* (GL*) respectively. Both values were
obtained from analyzing the 1D histograms (Figure 1).
Figure 2A displays the characteristic displacement histograms
of BT1, BT2, and BT4 in the high-conductance region H, and
Figure 2B illustrates, as an example, the characteristic
Figure 1. Conductance measurements of BT-end-capped oligoynes in
TMB/THF (4: 1, v/v) employing a STM-BJ (A−C) and a MCBJ (D−
F) setup. (A,D) Typical conductance distance traces of BT1, BT2, and
BT4. (B,E) 1D and (C,F) 2D conductance histograms generated from
2000 individual curves. The conductance traces were recorded with
Vbias = 0.035 V and a stretching rate of 58 nm s−1 (STM) or 5 nm s−1
(MCBJ). The asterisk indicates the noise level of the setup. The small
spike at log(G/G0) ≈ −2 in panel B is an artifact related to the
switching of the amplifier stage.
Several thousands of individual G−Δz traces were recorded
and subsequently analyzed further by constructing all-data
point histograms (without data selection), to extract statistically
significant results. Figure 1B displays the corresponding one-
dimensional (1D) histograms of BT1, BT2, and BT4 in a
semilogarithmic scale. We observe well-defined conductance
peaks GH, which shift toward lower values with increasing
number of CC− units. Gaussian fits lead to (316 136)·
10−5 G0, (81
9)·10−5 G0, and (20
6)·10−5 G0 as most
probable conductances of BT1, BT2, and BT4, respectively.
We notice that the values of most probable high conductances
GH were found to be independent of the oligoyne
concentration down to 100 nM. Furthermore, the shape of
the individual stretching traces, in particular the conductance
plateaus in the GH region, and the fluctuations of the
conductances as well as the most probable characteristic
displacement upon junction elongation ΔzH* (see Figure 2 for
definition) do not reveal a significant concentration depend-
ence. Only the probability of junction formation changes with
oligoyne concentration due to the limited availability of the
target molecules. For further details we refer to SI, Chapter 2.1
(Figure S18), which describes the characteristics of molecular
junctions formation of BT1 for concentrations ranging from 1
μM up to 1 mM as a representative case study. These
observations provide strong evidence in support of the
formation of single molecular junctions under our experimental
conditions.
D
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Table 1. Most Probable Conductance Values of Oligoyne (OY) Derivatives As Obtained From STM-BJ and MCBJ Experiments
log(G/G0) (STM)
log(G/G0) (MCBJ)
a
b
OY
GH
GM
GL
GH
GL
JFP
%
β (GH) nm−1
RC / kΩ
PY1
PY2
−3.4 0.1
−3.76 0.03
−4.4 0.1
−3.2 0.1
−3.5 0.1
−4.8 0.1
−5.0 0.1
−5.4 0.1
−2.8 0.1
−3.14 0.08
−2.5 0.2
−3.09 0.05
−3.7 0.1
−4.1 0.1
−4.5 0.2
−5.8 0.2
−3.3 0.1
−3.8 0.1
−
−3.2 0.2
−
−4.7 0.2
−4.8 0.2
−
−2.7 0.2
−3.1 0.2
−2.5 0.2
−2.6 0.2
−3.3 0.3
−5.8 0.2
∼ −7.0
100
100
100
60
−
3.1 0.4
∼2.5
205 120
PY4
−
−
−
−
−
−
−
−
−
−
−
−
−4.8 0.1
−4.9 0.6
−
−
NH21
NH22
CN1
CN2
CN4
SH1
SH2
BT1
BT2
BT4
−4.8 0.2
∼267
15 940 5580
∼13.5
−
−
−
95
63
−
−
37
1.7 0.1
∼3.18
−
45
−4.56 0.03
−4.65 0.05
−5.1 0.1
−5.52 0.05
−
−4.7 0.2
−
−4.9 0.2
−5.3 0.2
−6.0 0.2
90
100
100
100
100
2.9 0.2
∼11
3
a
b
JFP represents the single molecular junction formation probability. The β values were obtained using the average conductance values from STM
and MCBJ measurements and the characteristic length LJ (see Figure 6 for details of the definition of LJ). The β values of the NH2 and SH families
are tentative because they are based on measurements of just two derivatives each. The contact resistance RC per contact site was obtained from the
ordinate intersection at LJ = 0 based on the length dependence of log(G/G0) (cf. Figure 4A).
Table 2. Characteristic Lengths of Oligoyne Derivatives and Molecular Junctions As Obtained Experimentally and/or
Computed by DFT (see Figure 6 and SI for definitions)
a
b
c
d
e
d
e
OY
L, nm
LJ, nm
LJrel, nm
ΔzH*, nm
zH*= ΔzH* + zcorr, nm
ΔzL*, nm
zL* = ΔzL* + Δzcorr, nm
zL* − zH*, nm
f
f
f
PY1
PY2
PY4
0.98
1.24
1.76
1.26
1.52
1.49
1.76
2.28
1.31
1.57
1.31
1.56
2.08
1.40
1.66
2.18
1.74
2.00
1.91
2.18
2.70
1.77
2.03
1.79
2.04
2.56
1.15
1.41
1.93
1.49
1.75
1.66
1.93
2.45
1.52
1.78
1.54
1.79
2.31
0.56 0.05
0.68 0.04
1.45 0.13
0.68 0.07
0.82 0.07
0.58 0.3
1.06 0.05
1.18 0.04
1.95 0.13
1.18 0.07
1.32 0.07
1.10 0.3
0.69 0.05
0.82 0.05
−
0.91 0.10
1.24 0.02
−
1.19 0.05
1.32 0.05
−
1.41 0.14
1.74 0.02
−
0.13 0.05
0.14 0.05
−
0.23 0.14
0.42 0.07
−
NH21
NH22
CN1
CN2
CN4
SH1
SH2
BT1
BT2
BT4
0.80 0.12
0.67 0.13
0.88 0.04
1.10 0.09
0.88 0.01
1.06 0.08
1.43 0.10
1.30 0.12
1.17 0.13
1.38 0.04
1.60 0.09
1.38 0.01
1.55 0.08
1.93 0.11
−
−
−
−
−
−
1.26 0.07
1.36 0.20
1.1 0.2
1.3 0.1
1.6 0.2
1.76 0.07
1.86 0.19
1.62 0.18
1.77 0.11
2.11 0.16
0.38 0.07
0.26 0.19
0.24 0.18
0.22 0.11
0.18 0.16
a
DFT result for the distance L from the center of one anchor atom at one end of a fully extended isolated molecule to the center of the anchor atom
b
c
at the other end. LJ = L + 0.42 nm is the maximum possible length of the corresponding junction (see Figure 6 and Table S2). LJrel = LJ − 0.25 nm
is the corresponding electrode separation using the same definition of the zero of length used to define zH* and zL* . As shown in Table S2, this is
almost identical to the length of a fully extended junction just before breaking, obtained from DFT simulations of junction stretching. Estimated
from the experimental relative displacement histograms. Δzcorr is the snapback distance = 0.5 nm. For the PY series, the data in the ΔzL* column
are for the characteristic length of the middle conductance range ΔzM*.
d
e
f
displacement histogram of BT1 extended into the stability
range of the low-conductance state L. The data of Figure 2A
show uniform normal distributions with well-defined maxima.
The maxima correspond to the most probable characteristic
distances Δz*, which are measures of the most-probable
plateau lengths of the H conductance states of the three
molecules. Gaussian fits to the experimental data revealed the
following values of ΔzH*: (0.88 0.01) nm (BT1), (1.06
0.08) nm (BT2), and (1.43 0.10) nm (BT4), Table 2. The
widths of the three distributions appear to increase with
molecular length, which suggests larger variations in junction
geometry of BT4 as compared to BT1. No stretching trace
shorter than 0.5 nm was found, indicating that no direct
tunneling traces through the solution were observed.51
Therefore, we conclude that the molecular junction formation
probability in the high-conductance H-state of BT1, BT2, and
BT4 approaches 100%. Extending the analysis to 0.1 GL*
reveals a second maximum in the characteristic-displacement
distributions, which is attributed to the most probable
characteristic displacement ΔzL* of the low-conductance state
L. Figure 2B shows the corresponding data. We obtained (1.1
0.2) nm, (1.3 0.1) nm, and (1.6 0.2) nm for BT1, BT2,
and BT4, respectively (Table 2). Evaluating these data reveals
further that all traces transform from the H-state into the L-
state upon elongation of the molecular junction before it breaks
completely and reaches the noise level.
The most-probable absolute displacements zH* or zL* in an
experimental molecular junction formed between a gold STM-
tip and an Au(111) surface are obtained by adding the snap-
back distance Δzcorr (cf. refs 36, 55, and 56 and SI) to the
relative displacement Δz: zi* = Δzi* + Δzcorr, i = H, L.
Referring to our previous work with short tolane molecules
PY1, NH21, CN1, and SH1,36 we used Δzcorr = (0.5 0.1) nm.
Table 2 shows a comparison between the resulting values of
zH* and zL* and the theoretical estimations of the
corresponding electrode displacements of fully extended
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junctions just before breaking (denoted LJrel = LJ − 0.25 nm in
Table 2 and S2). This comparison demonstrates that the
experimental values of zH* are typically smaller than the
theoretical estimates of LJrel. On the other hand, zL* is
significantly larger than zH* and almost equal to LJrel. The
relationship between LJrel and a variety of other relevant lengths
is addressed in Tables 2 and S2 and Figure 6.
Conductance Decay and Variation with Displacement. To
gain further insight into the evolution of the molecular
conductance upon stretching, we calculated the most probable
conductances Gst at each relative displacement position Δz
from Gaussian fits to cross sections of the 2D histograms37
(Figure 3A). The individual conductance−distance traces, G
through space tunneling at the beginning of the stretching
process and interfere with the molecular junction conductance
in these regions. Upon increasing the distance between the gold
contacts, the contributions due to direct tunneling decrease,
and the slope δlog(Gst/G0)/δ(Δz) is exclusively determined by
the conductance through the molecular junctions. Transition
into the low-conductance state L is manifested in the master
curve by a coexisting range, which indicates a sequential
transition of the molecular junction from H to L, followed by
an additional range in the displacement plot that only reveals
the L state until rupture.
Changing the oligoyne concentration from 1 mM to 1 μM
does not lead to modifications of the plot of the statistically
averaged most probable conductance Gst versus the relative
displacement position Δz, except that no low-conductance
features and a much lower background contribution in the 1D
logarithmic histogram were found for BT concentrations below
0.1 mM. These observations strengthen the argument for the
formation of single-molecule junctions under our experimental
conditions. For the original data and further details we refer to
SI, Figure S18.
The distributions of the variation in conductance as shown in
Figure 3B and 3C were obtained by decomposing the 2D
histograms (Figure 1 and SI) into 1D histograms at different
relative displacements Δz and subsequent Gaussian fits.36 The
resulting distributions are rather narrow in displacement
regions dominated by the high conductance H - state (Figure
3B), and broaden in the L-state region (Figure 3C). Particularly
large fluctuations are observed in the transition region. We also
notice that increasing the molecular length L causes a
systematic broadening of variations in the entire displacement
region Δz, which clearly indicates a lower stability and less
uniform (single) molecular junctions.
Effect of Molecular Length and Anchoring Group on
the Conductance. We investigated next the influence of
molecular length (n = 1, 2, 4) and anchoring group on
conductance and stability of oligoyne-type molecular junctions
following the methodology described above for the three BT-
terminated compounds. The key parameters are summarized in
Tables 1 and 2. The original experimental data are shown in SI.
In the following paragraph we will describe experimental results
and correlations, which will be subsequently compared with
electronic structure and ab initio transport calculations.
Most Probable Single Junction Conductances. The PY-
terminated oligoynes revealed up to three distinct conductance
features upon stretching the molecular junctions,36,39 which
lead to most probable high (GH*), mid (GM*) and low (GL*)
conductance values. All three regions were resolved for
molecule PY1. We obtained the following results: GH*(PY1)
Figure 3. (A) Statistically averaged conductance−distance traces
(circles) with variation indicated by the standard deviation (bar) and
fitting of the traces (line) of BT1, BT2 (STM-BJ), and BT4 (MCBJ).
(B) Distribution of variations in conductance Δlog(G/G0) with
reference to the mean values (solid lines in panel A) at different
positions in the H conductance and (C) in the L conductance range
during stretching of BT1, BT2, and BT4. The data of BT2 nearly
coincide with BT1 in panel (C) and are therefore not shown.
versus Δz, and the 2D histograms, such as shown in Figure 1,
demonstrate that the plateaus of molecular junctions extend
over much longer distances than steps in the Au−Au
nanocontacts36 and that the conductances change during the
stretching process by one to two orders in magnitude. These
characteristics indicate that there are changes in conformation
and contact geometry or aggregation (e.g., π-stacking,
solvation) during the formation and elongation of a molecular
junction until rupture. Figure 3A−C displays the statistically
averaged conductances versus relative displacement master
curves log(Gst/G0) versus Δz together with the standard
deviations for BT1, BT2, and BT4 trapped between two gold
electrodes in the high- and low-conductance states, respectively.
We observed that Gst decreases in the high conductance state
linearly with slopes of 0.84 nm−1 (BT1), 0.61 nm−1 (BT2), and
0.31 nm−1 (BT4). The slope decreases with molecular length.
Compounds BT2 and BT4 show additional regions in 0 ≤ Δz
≤ 0.11 and 0 ≤ Δz ≤ 0.30 nm, which reflect contributions of
= (39
9)·10−5 G0, GM*(PY1) = (7.9
2.4)·10−5 G0 and
GL*(PY1) = (0.15 0.08)· 10−5 G0. The data of the high and
medium conductance states agree with literature reports39,61
within half an order of magnitude. In the case of the longer
oligoynes, PY2 and PY4, only two and one distinct
conductance regions were observed, which leads to GH*(PY2)
= (17.4 1.3)·10−5 G0, GM*(PY2) = (3.2 1.4)·10−5 G0 and
GH*(PY4) = (3.9
1.1)·10−5 G0 (Figure 4, Table 1). No
further conductance regions could be resolved for PY2 and
PY4 due to limitations in the sensitivity of our setup.
Oligoyne molecular wires end-capped with NH2- and SH-
anchoring groups demonstrated limited chemical stability for
chain lengths n > 2 (see SI). For the shorter members of both
families, we found two conductance regions with the most-
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a previous study with PY-terminated oligoynes.39 These
conductance data are based on the analysis of iT versus time
traces in the low bias regime, and differences in the most
probable conductances may arise from differences in the
statistical treatment of the data and from differences in tip
geometries, which affect the position of the Fermi energy
relative to the frontier orbitals.
We also observed that the effective contact resistances RC =
1/GC, determined by extrapolating the GH* versus LJ
dependencies toward LJ → 0, lead to the following sequence:
RC(BT) ≈ RC(SH) < RC(NH2) ≈ RC(PY) ≪ RC(CN) (Table
1). The values of βH and RC demonstrate that the different
anchor groups control the strength of the electronic coupling to
the metal leads, but also the position of the energy levels
involved in the electron transport across the single-molecule
junction as well as their coupling into the wire backbone. These
aspects will be discussed in detail in the theory section.
Finally, we mention that a decay value of the low
conductance region was accessible experimentally only for
one molecular family, βL(BT) = (3.1 0.2) nm−1. The other
oligoyne derivatives did not allow the extraction of statistically
reliable values. However, at a qualitative level, we may state that
the data available for several PY-, NH2-, SH- and BT- molecular
wires lead to an effective βL-value clustering around (3.0 0.5)
nm−1. The absolute values of the corresponding most probable
conductances GL* are less dependent on the nature of the
anchoring group as compared to GH* (for further details see
SI).
The widths of the distribution-variation of the junction
conductances at various elongations in the high as well as in the
low conductance regions increase in the following order: PY <
BT < NH2 < SH < CN for oligoynes with n = 1 and n = 2
(Figure 3B and SI). This trend confirms our previous results
with tolanes (n = 1), and is attributed to (i) the simultaneous
influence of nonuniform binding geometries (in particular for
members of the SH-family) and (ii) a decrease in binding
energy/junction stability (CN).36 The width of the distribution
increases also with the molecular length L within each family,
which is particularly attributed to the second factor (Figure 3C
and SI). The analysis of the low conductance state results in a
larger variation of the respective conductance data (Figure 3C
and SI), which correlates with the weaker interaction between
the different molecules and a larger variation in possible
binding geometries in these junctions. However, the overall
trend is the same as that in the high conductance region.
Stretching Distance and Junction Formation Probability.
Following the strategy outlined for BT-capped oligoynes we
constructed relative displacement histograms of all derivatives
(SI), and analyzed the characteristic length distributions upon
stretching in the high-conductance range, and down to the low-
conductance region. We obtained the most probable relative
characteristic distances Δzi*, the absolute stretching length zi*
(i = H, L) and the junction formation probabilities. These
results are summarized in Figure 5 and in Tables 1 and 2.
Analyzing the relative displacement (Δzi) distribution allows
quantification of the junction formation probability (JFP),36
e.g., the percentage of successfully created molecular junctions
out of all traces recorded (Table 1). These values reach 100%
for PY, BT, and SH. Comparing the five molecular families
reveals the following trend: CN < NH2 < SH ≈ PY ≈ BT. This
sequence may be considered as a measure of the stability of the
respective junctions. A more detailed analysis of the different
breaking pathways indicates that single molecular junctions
Figure 4. Most probable single junction conductance values GH* (A)
and GL* (B) of the five families of oligoynes as determined from the
analysis of 1D and 2D conductance histograms in dependence on the
length parameter LJ (see Figure 6 and SI for definition).
probable values GH* and GL* shown in Table 1. The high
conductance value of the NH2-terminated oligoynes with n = 1
is in good agreement with literature data.59,62 Published results
of the corresponding dithiolate derivatives SH158 and SH263
could not be confirmed. Possible reasons might be related to
data selection58,63 or a different experimental geometry
intrinsically existing in the iT versus time measurements,
which is the methodology chosen in ref.63 Just one region with
rather well-defined most probable single junction conductance
data GH* was found for the CN-terminated rods CN1, CN2
and CN4 (Figure 4, Table 1 and SI). The junction formation
probability of this family decreases with increasing molecular
length.
Figure 4 displays the dependencies of the most probable
conductances GH* and GL* versus the characteristic length LJ.
LJ is the DFT-predicted distance between the centers of the
two apex gold atoms in a fully extended molecular junction.
The corresponding data are compiled in Table 2. For further
details we refer to Figure 6 and the discussion in SI.
The analysis of the most probable high conductance values
GH* demonstrates an exponential dependence on distance for
oligoynes with PY, CN and BT anchoring groups according to
GH* = GC·exp(-βH·LJ). GC represents an effective contact
conductance reflecting the electronic coupling at the molecule-
electrode interface. βH is the attenuation constant, which
characterizes the electronic coupling in a specific molecular
backbone in function of its length. The experimentally
determined βH values range between (1.7 0.1) nm−1 (CN)
to ∼3.18 nm−1 (SH). The following trend is tentatively
observed βH(CN) < βH(NH2) < βH(BT) ≈ βH(PY) < βH(SH)
(Table 1). We notice that the data set of the NH2 and SH-end-
capped oligoynes are rather limited. NH24 and SH4 could not
be measured successfully due to limited stability of these
compounds under our experimental conditions. Therefore, the
β−values of the NH2- and SH-families should be considered
with caution.
The experimental values of the decay parameter βH of our
study compare with those of other molecular bridges as follows:
saturated alkanes10,33,34 (7 - 11 nm−1) > oligophenyls64,65 (OP,
3.5 - 5 nm−1) > oligo(phenylene-ethynylenes)13,58−60 (OPEs,
2.0 - 3.4 nm−1) > oligophenyleimine66 (OPI, 3 nm−1) >
carotenoid polyenes67,68 (1.7 - 2.2 nm−1) > oligo(phenylene-
vinylenes)10,69 (OPVs, 1.7 - 1.8 nm−1) > benzene-furan
oligoaryls69 (1.1 - 1.3 nm−1) > oligothiophenes70 (OT, 1.0
nm−1) > carbodithioate-capped OPEs58 (CT, 0.5 nm−1) >
porphyrin oligomers63 (0.4 nm−1) > pyridyl-capped oligoynes39
(0.06 nm−1). Our βH values are in the same range as those of
typical conjugated wires, such as OPEs, OPVs and OPIs. We
could not confirm the low βH values reported by Wang et al. in
G
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pulling curves for each molecule, 50 initial values of electrode
separation (denoted x0Au−Au) were chosen in increments of 0.04
nm, with the shortest distance approximately equal to the
molecular length L minus the thickness of four layers of gold,
i.e., ∼ L − 1 nm. For geometry optimization, the first two layers
at the base of each pyramid were fixed, and the remaining three
layers of each pyramid (closest to the molecule) were allowed
to relax. Geometry optimization was carried out using the DFT
package SIESTA53 (for further details see SI). After geometry
optimization the electrode separation changed slightly from the
Figure 5. Dependence of the most probable characteristic length zi* of
molecular junctions, i = H,L, on LJrel (see Figure 6 for definition of
LJrel) in the (A) high conductance range 0.7 G0 < G < 0.1 GH and in
the (B) low conductance range 0.7 G0 < G < 0.1 GL. Each data point
represents the average value of measurements carried out using at least
three different bias values Vbias (0.025 to 0.170 V). The error bars
represent their standard deviations.
initial value x0
to a final value xAu−Au.
Au−Au
Binding Geometry and Binding Energies. For each initial
tip separation x0Au−Au, the molecule was positioned with its
anchor rings facing the surface of the pyramids and ∼0.2 nm
away from the local pyramid surface (Figure 6). To avoid
artifacts in the geometry optimization due to symmetry, the
molecule was initially slightly shifted from the midpoint (0.1
nm) toward one of the electrodes. A selection of these relaxed
geometries is shown in Figure 7 for the case of BT4 single-
molecule junctions.
with SH, PY, and BT termini break with a high percentage in
the low-conductance state, while NH2 and CN-terminated
wires rupture already upon elongation in the high-conductance
region (see SI for details). This trend represents an additional
stability marker of the respective molecular junction.
DFT Calculations and Analysis of Junction Evolution.
To provide further insight into the experimentally observed
trends and the evolution of molecular junctions, we performed
theoretical calculations using a combination of DFT and a
nonequilibrium Green’s function formalism. For each of the
molecular families, corresponding to the five distinct anchor
groups, each junction was regarded as an “extended molecule”
composed of a single molecule attached to two (111) directed
pyramids of 35 gold atoms. For a junction geometry such as
that shown in Figure 6, we defined the electrode separation
xAu−Au to be the center-to-center distance between the apex
atoms of the two opposing pyramid tips. To generate complete
Figure 7. Examples of junction evolution of oligoyne derivatives BT4
showing key configurations.
To demonstrate qualitatively the energy changes during the
stretching process, we computed the junction energy EJ, which
is defined as the total energy of the relaxed extended molecule
(obtained from SIESTA) relative to the total energy of the fully
broken junction when the molecule binds only to one of the
electrodes (e.g., BT-VI in Figure 7). We investigated 50
different junction geometries for each oligoyne derivative.
Figure 8 displays the junction energies for the BT series plotted
against the electrode separation. To compare junction energies
of molecules with different backbone lengths we define the
quantity xn = xAu−Au − Δ(n − 1), where n is the number of
triple bonds in the molecule and Δ = 0.26 nm. The latter
Figure 6. Schematic representation of the “extended molecule” of BT1
in contact with conducting leads. This illustrates the relevant distances
and lengths L, xAu−Au, LJ, dAu−Au, and LJrel, which were computed after
the DFT-based structure has relaxed. L is the distance from the center
of an anchor atom at one end of the fully extended isolated molecule
to the center of the anchor atom at the other end. At an arbitrary stage
during the theoretical junction stretching, the theoretical electrode
separation xAu−Au is defined as the distance between the center of the
two gold apex atoms. LJ is defined to be the value of xAu−Au when the
junction breaks. The distance dAu−Au 0.25 nm is the electrode
separation of a monatomic gold contact, when the junction has the
conductance G0. This is the gold−gold distance at which the bond
between apex atoms is neither compressed nor stretched. LJrel is the
theoretically estimated relative displacement of a junction containing a
fully extended molecule, arising when the zero of relative displacement
(Δz = 0) corresponds to an apex-atom separation of dAu−Au and is
defined as LJrel = LJ − dAu−Au (see Table S2). Panel B shows the
structure of the gold electrodes used in the simulations.
Figure 8. Junction energies for the BT series as a function of the scaled
electrode separation xn = xAu−Au − Δ(n − 1), where n is the number of
triple bonds and Δ = 0.26 nm, the change in length of a molecule
when n increases by unity.
H
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represents the change in length of a molecule when n increases
by unity. Results for the PY, CN, NH2, and SH families are
shown in Figures S37, S39, S41, and S43.
no direct bond between the chain and the gold electrodes was
found. Upon increasing the separation xAu−Au, the molecules
undergo a sequence of sliding configurations during the
stretching simulation, with the aromatic rings facing the surface
of the gold pyramids, as shown in Figures 7 and S35. When the
electrode separation xAu−Au reaches approximately two-thirds of
the molecular length L, the anchor atom on one side jumps to
the top position of one pyramidal gold contact, while the other
end of the molecule continues to slide down the gold surface as
before. Examples are BT-III (Figure 7) and NH2-III, PY-III,
CN-III, and SH-III (Figure S35). In some cases, such as PY-IV,
CN-IV, and SH-IV (SI, Figure S35), the molecule contorts to
bind to atop positions of the gold pyramid. This feature is
particularly pronounced for the PY- and CN-end-capped series.
As the electrode separation approaches the molecular length L,
the molecules jump into the gap and bind to an apex gold atom
of both pyramids (BT-V, PY-V, NH2−V, CN-V, SH-V) before
the leads are too far apart to bridge, and the junction is broken
(BT-VI, PY-VI, NH2−VI, CN-VI, SH-VI).
To relate the experimentally measured most-probable
breaking lengths, zi*, with the theoretically computed lengths,
Table 2 shows the comparison between the experimentally
measured lengths zH*, zL* and the computed length LJrel, where
LJrel is the maximum possible length of a junction containing a
fully extended molecule. The most probable experimental
stretching lengths in the high conductance regime, zH*, are
smaller than LJrel, whereas the low-conductance values of zL*
are approximately equal to LJrel. The average differences zL* −
zH* vary between 0.13 nm for PY and up to 0.38 nm for SH
and are comparable with the 0.24 nm height of a typical
monatomic gold step. Literature reports suggest that strong
interactions between contact leads and the anchoring group
could cause major rearrangements or even the pulling out of
gold atoms.36,71 The formation of a fully extended molecular
junction may also be followed by the creation of intermolecular
π-stacking assemblies in the gap.72,73
The fact that the plots of a single family, independent of the
molecular length, collapse onto a single curve demonstrates
that energies are primarily determined by the anchor group and
are only weakly dependent on the length of the oligoyne bridge.
In all cases, as the anchor group slides across the pyramidal
tip (SIDE configurations), the junction energy was found to
oscillate as a function of xn, with a period which approximately
coincides with the gold layer spacing. In an attempt to
quantitatively relate to experiments, we computed the binding
energies between the molecule and the two gold electrodes
using the counterpoise method in the fully broken confi-
VI
guration (e.g., BT-VI shown in Figure 7), denoted as Eb and
V
in the bridge stage (e.g., BT-V in Figure 7), denoted as Eb
(Table 3).
Table 3. Binding Energies Calculated between a Molecule
and Two Electrodes for n = 1−4 Cases for Two
Configurations
(eV)
n
BTn
PYn
SHn
CNn
NH2n
VI
Eb,1
0.44
0.77
0.44
0.84
0.41
0.78
0.41
0.84
0.41
0.40
0.82
0.42
1.12
0.43
1.19
0.41
1.24
0.50
1.51
3.00
1.48
2.98
1.47
3.02
1.47
3.13
1.51
0.35
0.78
0.34
0.88
0.33
0.94
0.35
0.94
0.41
0.37
0.66
0.34
0.66
0.33
0.60
0.33
0.34
0.30
1
V
Eb,1
VI
Eb,2
2
3
V
Eb,2
VI
Eb,3
V
Eb,3
VI
Eb,4
4
V
Eb,4
E
̅
−
b
VI
V
Typically, we find that Eb is approximately half of Eb
because only one of the anchor−gold bond breaks at junction
rupture. Across the five anchoring groups we obtained the
following trend in the average binding energies E : Au−
̅
Comparison of zH* with LJrel (Table 2) demonstrates that in
the high-conductance regime, none of the oligoyne derivatives
assumes a fully stretched molecular junction between the two
gold leads. Based on this comparison between zH* and LJrel, we
propose that the high-conductance region involves SIDE
configuration and multicoordinated sites near the tip of the
adjacent gold pyramids. We may distinguish between two
groups of oligoynes. The ratio of zH*/LJrel is rather high
(>90%) for molecular junctions composed of PY-, SH-, and
BT-end-capped derivatives indicating stable, slightly tilted (with
respect to a fully upright) configurations. The corresponding
ratios of NH2 (<80%) and CN (<65%) derivatives are lower.
We also notice that junctions formed by longer molecular wires
appear to be less stable than shorter ones as indicated by the
lower junction formation probability and a lower ratio zi*/LJrel.
Since the values of zL* are comparable with LJrel, we suggest
that the experimentally observed low-conductance states
represent junction configurations sampled after the “jump” of
the anchor atom on one side of the top position of a gold
pyramid, while the second atom (anchor group) continues to
slide down the gold surface until complete rupture. These
regions are depicted by the configurations BT-III (Figure 7)
and PY-III and SH-III (Figure S35) and by those samples at
larger electrode separations. A low-conductance region was also
found for the NH2-end-capped oligoynes (Figure 4 and SI),
which might indicate that the transition from a SIDE-SIDE into
b
N(NH2) < Au−S(BT) ≈ Au−N(CN) ≈ Au−N(PY) ≪ Au−
S(SH). The NH2 anchor binds least strongly, due to steric
hindrance caused by the amino group hydrogen atoms. If the
binding energies are an indicator of the probability of junction
formation, then the above results suggest that BT, PY, and SH
should form junctions with a higher probability than NH2, in
agreement with the experimentally observed low junction
formation probability for NH2. On the other hand, our
experimental findings for the low junction formation probability
of CN do not correlate with the theoretically predicted high
binding energy of the CN group on gold. This suggests that
other factors affect the junction formation, such as competition
with solvent molecules and the resilience of an anchor group to
defects in the gold leads. Typically we find that the thiol binds
with the largest binding energy, although in the calculation we
did not cap the molecule with hydrogen after separation from
the gold.
Junction Evolution. We now describe details of junction
evolution, movies of which are presented in the SI. Figure 7
shows snapshots of relaxed geometries for BT4. Geometries for
PY4, NH24, CN4, and SH4 are shown in Figure S35. The
initial electrode separations xo
are: 0.62 nm (PY), 0.905
Au−Au
nm (NH2), 1.132 nm (CN), 0.968 nm (SH), and 0.956 nm
(BT). Initially the carbon atoms at opposite ends of the
oligoyne chain tend to bind directly to the tip of the gold
pyramids. As shown in Figure 7, BT-I is an exception, for which
I
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Figure 9. (A) Scaled transmission curve log(A·T(E)) versus (E−EF) obtained for BT4 at various stages of the stretching process and (B) the
corresponding scaled conductance log(G/G0) versus xAu−Au trace (scaling factor 0.10, see text for details). The vertical dotted line in panel (A) marks
the shifted Fermi energy EF. The thin horizontal line in panel (B) shows the median of the marked conductance points. The roman numeral dotted
lines in panel (B) correspond to various geometries shown in Figure 7 (BT-I to BT-VI). Panel (C) shows the histogram generated from data plotted
in (B).
an atop-SIDE junction configuration may take place even at an
earlier stage of junction elongation.
between the anchors and the gold electrodes and thereby
decrease the conductance relative to the generalized-gradient
approximation (GGA) values. Comparing experimental and
computed data of the five oligoyne families, we obtained A =
0.10 (see also ref 36). This scaling factor is smaller than that in
our previous calculations,36 because we fitted a single scaling
parameter to five families of molecules instead of to data from
only four individual molecules. Furthermore, we also used an
improved model for the electrodes in the present work (Figure
6). For the same reason the corrections in EF are slightly
modified. The corrections to EF indicate that the transport
through molecular junctions of PY- and CN-end-capped
oligoynes is due to nonresonant tunneling through the tails
of the respective LUMO states. This is in agreement with
results reported for related molecules.39,51,55 Transport through
junctions with SH, NH2, and BT-termini appears to proceed via
the tail of the nearby HOMO state, which is also supported by
data obtained with similar molecular wires.48,62,76
Transmission Curves and Single Junction Conductances.
With the above qualitative understanding of junction evolution
in end-capped oligoynes, we discuss next the theoretical
transmission curves and electrical conductances. The under-
lying DFT mean-field Hamiltonian was used to compute the
quantum mechanical electron transmission coefficient T(E) via
the SMEAGOL package. For such transport calculations, the
base layers of the pyramids were attached on both sides to eight
layers of (111)-oriented bulk gold with each layer consisting of
6 × 6 atoms and a layer spacing of 0.235 nm (Figure 6). These
layers were then used to extend the gold electrodes to infinity.
Figure 9A shows selected plots of T(E) versus the energy (E−
EF) for the BT4. The corresponding plots of T(E−EF) versus
(E−EF) for the entire other families of molecules are shown in
Figures S36−S45.
The conductance was then obtained from the electron
transmission coefficient T(E) evaluated at the Fermi energy EF
multiplied by a scaling factor A (see below). We note that DFT
does not usually predict correctly the alignment of the frontier
molecular energy levels in the junction relative to the Fermi
energy. To overcome this deficiency, self-energy and screening
corrections are required.55,74,75 However, these corrections are
typically obtained for locally optimal configurations in vacuum
between rather flat contacts. These conditions do not match
our experimental situation (in solution with either one (STM)
or two (MCBJ) pyramid-shaped contacts). The correction
depends sensitively on the precise coordination of the bridging
gold atom, on the relative strengths of binding to the two gold
electrodes, and on the position and orientation of the image
charges.75 In view of these uncertainties, we adopted the more
empirical approach, which involves computing the iT−Vbias
We computed single-molecule junction conductances as a
function of the electrode separation xAu−Au for the five oligoyne
families. The complete set of data including the generated
movies illustrating the evolution of the junction configurations
and the corresponding transmission functions of the five
oligoynes is given in the SI.
As an example, Figure 9A displays selected (out of 50) scaled
transmission curves of BT4 computed at various stages of the
stretching processes. Panel 9B shows the electrical conductan-
ces at each electrode separation xAu−Au obtained by evaluating
the scaled transmission coefficient A·T(E−EF) at the Fermi
energy E = EF. Specific values of log(G/G0) at various stages of
the pulling process (Figure 7) are indicated by the vertical
dotted lines in Figure 9B. The evolution of the dimensionless
junction conductance traces with the electrode separation
xAu−Au demonstrates that the conductance generally decreases
with xAu−Au and that the lengths of the plateaus increase with
molecular length L (Figures 9 and S36, S38, S40, S42 and S44).
Both trends agree with our experimental observations (Figures
1 and 4 and Table 2, see also SI). A more detailed evaluation of
the computed conductance curves suggests that the fluctuations
increase upon approaching the transition from SIDE-SIDE to
SIDE-atop configurations of the junction (Figure 7), which
could be attributed to the characteristic properties of the high
and low conductance regions.
characteristics for a range of Fermi energies EF in the vicinity
DFT
of the DFT-predicted Fermi energy EF
and adjusting the
Fermi energy EF so that DFT-SMEAGOL-computed current−
voltage characteristics agree with the experimentally measured
iT−Vbias curves. The method was introduced for tolanes
(oligoynes with n = 1) in ref 36 and is detailed in the SI.
Employing this approach, we estimated the following
corrections in EF−EFDFT: −0.2 eV (BT), −0.65 eV (PY), 0.1
eV (SH), −0.2 eV (NH2), and −1.0 eV (CN) (see SI for
details). To obtain a reasonable fit, it was also necessary to
multiply the computed electron transmission coefficient by a
single common scaling factor A, which accounts empirically for
the fact that real electrodes contain defects and the well-known
deficiencies in DFT. The latter include particularly the absence
of van der Waals interactions, which could increase the distance
The conductance values plotted in Figure 9B were then used
to construct conductance histograms (Figure 9C). The most
probable conductance values of the high-conductance state
log(G/G0) for each family of molecules are plotted as a
function of LJ in Figure 10. The slopes of these curves yield the
J
dx.doi.org/10.1021/ja4015293 | J. Am. Chem. Soc. XXXX, XXX, XXX−XXX

Journal of the American Chemical Society
Article
comp
computed values βH
(BT) = 1.7 nm−1, which is slightly
the simulations, as the molecule detaches from the electrodes,
the sulfur termini become thiyl free radicals, which leads to the
alignment of the HOMO resonance with EF. In contrast, the
radical species is not isolated under experimental conditions but
surrounded by an environmental reservoir, which neutralizes
excess charges and/or free radicals, respectively.77
smaller than the experimental values βH(BT) = (2.9
0.2)
nm−1 (Table 1, Figure 4).
To shed further light on the origin of the low-conductance
states, we compare the results of the computed scaled
conductances log(G/G0) versus xAu−Au traces (Figures 9 and
S36, S38, S40, S42 and S44) with the values of zL*, the
experimentally observed most probable absolute displacements
in the low-conductance regions (Table 2). Both values are
related to each other according to xAu−Au = zL* + 0.25 nm. With
this correspondence, we note that the experimental values of
(zL* + 0.25) of the four families BT, PY, SH, and NH2 coincide
with the ends of the plateaus and the beginning of the regions
of low conductances in the computed conductance traces
(Figure 9 and S36, S38, S40, S42 and S44). From the movies
provided in the SI, the ends of the plateaus correspond to
anchor groups binding to the top atoms of the pyramidal
contacts. Therefore this is one possible contribution to the
measured low conductances. However since low conductances
are measured also at separations greater than the most probable
value zL* these cannot be single-molecule configurations unless
an Au atom is pulled from the contact. Alternatively, such low-
conductance states could arise from the π−π stacking of two or
more molecules, with one molecule bound to the lower contact
and the other bound to the upper contact.
Figure 10. Plot of the most probable experimental (full symbols) and
computed (open symbols and lines) conductance values log (G/G0)
versus the characteristic junction length LJ for each family of
molecules.
The plots of log(G/G0) versus LJ for the other oligoyne
families are shown in Figure 10 and yield the following
computed βH values for the high-conductance regions:
βHcomp(PY) = 2.2 nm−1, βHcomp(NH2) = 1.8 nm−1, βHcomp(SH)
= 1.2 nm−1, and βHcomp(CN) = 0.4 nm−1. The trends in the
computed conductances are in qualitative agreement with
comp
experimental data, although the theoretical βH
values are
consistently smaller than the experimental ones. Within the
present theory of phase-coherent tunneling, the latter is a
reflection of the well-known tendency for DFT to under-
estimate the size of the HOMO−LUMO gap, which leads to an
underestimation of the decay rate of the transmission
coefficient with length. Furthermore, the theoretical calcu-
lations were performed in vacuum, whereas the experiments
were carried out in the presence of solvent. In the case of NH2
and thiol-terminated oligoynes differences may also arise,
because estimates of βH(NH2) and βH(SH) are based on only
two experimental conductance values (n = 1, 2). We also note
that the binding energies and transport calculations do not
explain the experimentally observed lower stability of the CN-
terminated molecular junctions as compared to those with PY
anchors.
In contrast with the theoretical pulling curves, which contain
rather flat plateaus, the experimental conductance−trace curves
tend to decrease during stretching. This difference is likely to
arise, because the shape of the tip is unknown and is modeled
theoretically as a regular pyramid. In practice, other shapes may
arise. The presence of a solvent may also tend to displace the
molecule, particularly at longer separations. Furthermore in the
simulations, the Fermi energy is assumed to be constant during
the pulling process, whereas image charges may cause the
HOMO−LUMO gap to increase as the junction length
increases, thereby causing the conductance to decay with
increasing separation.
Despite these limitations, additional common trends between
experiment and simulations were found. The high-conductance
plateaus for the BT series (Figures 9B and S44) are flat and less
noisy than others (Figures S36, 38, 40, and 42). Furthermore,
Figure S40 shows that the plateaus of the PY series are steeper
than all others. The SH derivatives shown in Figure S42
represent an exception, because the tail of the conductance
plateaus increases as the molecular wire approaches breaking
(see SI), whereas the experimental 2D conductance displace-
ment histograms show a decreasing trend with the low-
conductance state at the end. This difference arises because in
CONCLUSIONS
■
By using rational molecular design and synthesis, combined
with STM-BJ and MCBJ techniques, we have comprehensively
studied diaryloligoynes terminated with the novel anchor group
BT for the attachment to gold electrodes. Comparative studies
were also carried out with CN, NH2, SH, and PY anchors. We
find that the shorter n = 1 (tolane) and n = 2 (butadiyne)
molecules are all stable under ambient conditions. For the n = 4
(tetrayne) analogs, the CN, pyridyl, and BT derivatives are
stable; however, the NH2 and SH derivatives rapidly
decompose at room temperature, presumably due to the
terminal groups reacting intermolecularly with the oligoyne
backbone. Overall, our joint experimental and theoretical
investigations of the length dependence and anchor-group
dependence suggest that BT-terminated oligoynes are parti-
cularly attractive: They display the highest probability of
junction formation and electrical conductance values which are
higher than reported values of other conjugated molecular wires
of similar length. Based on concentration-dependent studies of
the target molecules between 100 nM and 1 mM, we provide
convincing evidence for the formation of single-molecule
junctions in the high-conductance state under our experimental
conditions. The low-conductance state is attributed to two
possible scenarios: (i) single-molecule junctions involving the
pulling out of gold atoms from the contact leads or (ii)
multimolecular junctions involving π−π stacking.
Comparable experimental results were obtained using STM-
BJ and MCBJ setups, especially for the high-conductance states:
the experimental βH values range between 1.7 nm−1 (CN) to
3.2 nm−1 (SH), with the following tentative trend βH(CN) <
βH(NH2) < βH(BT) ≈ βH(PY) ≈ βH(SH). Theoretical values
were lower, in the range of 0.4−2.2 nm−1, with βHcomp(CN) <
βHcomp(SH) < βHcomp(NH2) ≈ βHcomp(BT) ≈ βHcomp(PY). To
compare with experiments, we calculated whole conductance−
K
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Journal of the American Chemical Society
Article
Schonenberger, C.; Calame, M. J. Am. Chem. Soc. 2008, 130, 1080−
1084.
(9) Newton, M. D.; Smalley, J. F. Phys. Chem. Chem. Phys. 2007, 9,
trace curves, whose evolution with electrode separation is
demonstrated for each molecular family in full movies. We
show further that the sliding of the anchor groups across the
pyramidal gold electrodes leads to oscillations in both the
electrical conductance and the junction energies of the
molecular wires. These conductance traces were used to
generate conductance histograms, which compare favorably
with the high-conductance regions of the experimental
histograms obtained from STM-BJ and MCBJ measurements.
To summarize, this study has shown that stable oligoynes
with up to eight acetylenic carbons in the backbone (i.e.,
tetraynes) can be synthesized with different end groups that are
suitable for anchoring the molecules to gold electrodes. BT
anchor groups are shown to be particularly beneficial in this
regard. Oligoynes are now established as a versatile class of π-
conjugated molecular wires for the fabrication of highly
conductive nanoscale junctions.
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ASSOCIATED CONTENT
* Supporting Information
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■
S
Eur. J. 2002, 8, 408−432.
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Experimental part: synthesis and characterization of oligoyne
compounds, UV−vis absorption and NMR spectra, X-ray
crystallography, stability tests, transport measurements and data
analysis procedures, conductance dependence on concentra-
tion. Computational part: simulation for isolated molecules,
length scale, electrical conductance and transmission curves of
molecules within junctions, movies of junction evolution. This
material is available free of charge via the Internet at http://
pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
c.lambert@lancaster.ac.uk; m.r.bryce@durham.ac.uk; thomas.
wandlowski@dcb.unibe.ch
■
(25) Simpkins, S. M. E.; Weller, M. D.; Cox, L. R. Chem. Commun.
2007, 4035−4037.
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Author Contributions
⊥These authors contributed equally.
Phys. Chem. 2007, 58, 535−564.
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Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
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■
This work was generously supported by the Swiss National
Science Foundation (200021-124643; NFP 62), the German
Science Foundation (priority program SPP 1243), the UK
EPSRC, the EC FP7 ITN “FUNMOLS” project no. 212942,
and the University of Bern. P.M.G. also acknowledges support
́
from CONACyT, Mexico (209297).
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